The primary purpose of Renewable Portfolio Standard (RPS) is to facilitate investment in renewable energy technology. Since emission trading program has similar purpose, it is conceivable to attempt to link RPS and emission trading program through interlinked markets. RPS in Korea with single REC and emission allowance markets has particular advantages for constructing linkages between two markets. This paper provides a real option model to examine investment effects of linkage of RPS to the trading program. Emission permit price and REC price are assumed to follow stochastic processes and renewable investment is irreversible. The result shows that linked market provides further incentive for renewable investment by raising managerial flexibility for power companies.